Execution of AUVprocess_main version 1.86 at 2018-05-26T00:04:57Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2017, ['121.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2017.121.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/navigation.nc') Creating vector time with 405034 elements. Creating vector mPos_x with 405034 elements. Creating vector time with 405034 elements. Creating vector mPos_y with 405034 elements. Creating vector time with 405034 elements. Creating vector mDepth with 405034 elements. Creating vector time with 405034 elements. Creating vector mGpsNorth with 405034 elements. Creating vector time with 405034 elements. Creating vector mGpsEast with 405034 elements. Creating vector time with 405034 elements. Creating vector mGpsValid with 405034 elements. Creating vector time with 405034 elements. Creating vector mPhi with 405034 elements. Creating vector time with 405034 elements. Creating vector mTheta with 405034 elements. Creating vector time with 405034 elements. Creating vector mPsi with 405034 elements. Creating vector time with 405034 elements. Creating vector mOmega_x with 405034 elements. Creating vector time with 405034 elements. Creating vector mOmega_y with 405034 elements. Creating vector time with 405034 elements. Creating vector mOmega_z with 405034 elements. Creating vector time with 405034 elements. Creating vector mPsaRange with 405034 elements. Creating vector time with 405034 elements. Creating vector mAltitude with 405034 elements. Creating vector time with 405034 elements. Creating vector multibeamAltitude with 405034 elements. Creating vector time with 405034 elements. Creating vector mDvlAltitude with 405034 elements. Creating vector time with 405034 elements. Creating vector mEchoAltitude with 405034 elements. Creating vector time with 405034 elements. Creating vector mEchoHorizRange with 405034 elements. Creating vector time with 405034 elements. Creating vector mEchoAltitudeLast with 405034 elements. Creating vector time with 405034 elements. Creating vector mEchoHorizRangeLast with 405034 elements. Creating vector time with 405034 elements. Creating vector mEchoNumOfPings with 405034 elements. Creating vector time with 405034 elements. Creating vector nadirCnts with 405034 elements. Creating vector time with 405034 elements. Creating vector obstacleCnts with 405034 elements. Creating vector time with 405034 elements. Creating vector nGoodNadirBeams with 405034 elements. Creating vector time with 405034 elements. Creating vector medianNadirBeamNo with 405034 elements. Creating vector time with 405034 elements. Creating vector mWaterSpeed with 405034 elements. Creating vector time with 405034 elements. Creating vector mDvlValid with 405034 elements. Creating vector time with 405034 elements. Creating vector mDvlNewData with 405034 elements. Creating vector time with 405034 elements. Creating vector mDeltaT with 405034 elements. Creating vector time with 405034 elements. Creating vector nfix with 405034 elements. Creating vector time with 405034 elements. Creating vector efix with 405034 elements. Creating vector time with 405034 elements. Creating vector filter_north with 405034 elements. Creating vector time with 405034 elements. Creating vector filter_east with 405034 elements. Creating vector time with 405034 elements. Creating vector filter_depth with 405034 elements. Creating vector time with 405034 elements. Creating vector north_current with 405034 elements. Creating vector time with 405034 elements. Creating vector east_current with 405034 elements. Creating vector time with 405034 elements. Creating vector speed_bias with 405034 elements. Creating vector time with 405034 elements. Creating vector heading_bias with 405034 elements. Creating vector time with 405034 elements. Creating vector latitude with 405034 elements. Creating vector time with 405034 elements. Creating vector longitude with 405034 elements. Creating vector time with 405034 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/navigation.nc'); processNav(): median of positive valued depths = 31.275 processNav(): Finding depths less than 218.9248 and times > 0 processNav(): length(Nav.depth) = 405034 processNav(): length(gindx) = 405034 Processing GPS navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/gps.nc') Creating vector time with 13039 elements. Creating vector hours with 13039 elements. Creating vector time with 13039 elements. Creating vector minutes with 13039 elements. Creating vector time with 13039 elements. Creating vector seconds with 13039 elements. Creating vector time with 13039 elements. Creating vector centiSeconds with 13039 elements. Creating vector time with 13039 elements. Creating vector latitude with 13039 elements. Creating vector time with 13039 elements. Creating vector longitude with 13039 elements. Creating vector time with 13039 elements. Creating vector quality with 13039 elements. Creating vector time with 13039 elements. Creating vector numberOfSatellites with 13039 elements. Creating vector time with 13039 elements. Creating vector hdop with 13039 elements. Creating vector time with 13039 elements. Creating vector antennaHeight with 13039 elements. Creating vector time with 13039 elements. Creating vector geoHeight with 13039 elements. Creating vector time with 13039 elements. Creating vector dgpsDataAge with 13039 elements. Creating vector time with 13039 elements. Creating vector dgpsRSID with 13039 elements. Creating vector time with 13039 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/gps.nc'); processGPS(): *** skipping bad position (lat,lon) = 22.4885, -97.0786 processGPS(): *** skipping bad position (lat,lon) = 22.4656, -97.0375 processGPS(): *** skipping bad position (lat,lon) = 22.4427, -96.9964 processGPS(): *** skipping bad position (lat,lon) = 22.4199, -96.9554 processGPS(): *** skipping bad position (lat,lon) = 22.3971, -96.9144 processGPS(): *** skipping bad position (lat,lon) = 22.3744, -96.8735 processGPS(): *** skipping bad position (lat,lon) = 22.1281, -96.4297 processGPS(): *** skipping bad position (lat,lon) = 22.106, -96.3898 processGPS(): *** skipping bad position (lat,lon) = 21.9963, -96.1915 processGPS(): *** skipping bad position (lat,lon) = 21.9746, -96.1522 processGPS(): *** skipping bad position (lat,lon) = 21.9312, -96.0736 processGPS(): *** skipping bad position (lat,lon) = 21.9096, -96.0344 processGPS(): *** skipping bad position (lat,lon) = 21.8666, -95.9564 processGPS(): *** skipping bad position (lat,lon) = 21.8451, -95.9175 processGPS(): *** skipping bad position (lat,lon) = 21.8237, -95.8787 processGPS(): *** skipping bad position (lat,lon) = 21.8024, -95.8399 processGPS(): *** skipping bad position (lat,lon) = 21.7811, -95.8012 processGPS(): *** skipping bad position (lat,lon) = 21.7598, -95.7626 processGPS(): *** skipping bad position (lat,lon) = 21.7386, -95.724 processGPS(): *** skipping bad position (lat,lon) = 21.7175, -95.6856 processGPS(): *** skipping bad position (lat,lon) = 21.5916, -95.4564 processGPS(): *** skipping bad position (lat,lon) = 21.5708, -95.4185 processGPS(): *** skipping bad position (lat,lon) = 21.55, -95.3806 processGPS(): *** skipping bad position (lat,lon) = 21.5293, -95.3428 processGPS(): *** skipping bad position (lat,lon) = 21.5087, -95.3052 processGPS(): *** skipping bad position (lat,lon) = 21.4881, -95.2676 processGPS(): *** skipping bad position (lat,lon) = 21.4675, -95.23 processGPS(): *** skipping bad position (lat,lon) = 21.3858, -95.0805 processGPS(): *** skipping bad position (lat,lon) = 21.3655, -95.0433 processGPS(): *** skipping bad position (lat,lon) = 21.3452, -95.0062 Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/parosci.nc') Creating vector time with 795175 elements. Creating vector depth with 795175 elements. Creating vector time with 795175 elements. Creating vector temp with 795175 elements. Creating vector time with 795175 elements. Creating vector pressure with 795175 elements. Creating vector time with 795175 elements. Creating vector temp_period with 795175 elements. Creating vector time with 795175 elements. Creating vector pres_period with 795175 elements. Creating vector time with 795175 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.36557 max(Depth.data) = 102.0458 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.36557 max(Depth.data) = 102.0458 Processing hs2 backscattering and chlorophyll fluorescence data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/hydroscatlog.nc') Creating vector time with 323987 elements. Creating vector Seconds with 323987 elements. Creating vector time with 323987 elements. Creating vector HundrethsOfSeconds with 323987 elements. Creating vector time with 323987 elements. Creating vector Snorm1 with 323987 elements. Creating vector time with 323987 elements. Creating vector Snorm2 with 323987 elements. Creating vector time with 323987 elements. Creating vector Snorm3 with 323987 elements. Creating vector time with 323987 elements. Creating vector Gain_Status_1 with 323987 elements. Creating vector time with 323987 elements. Creating vector Gain_Status_2 with 323987 elements. Creating vector time with 323987 elements. Creating vector Gain_Status_3 with 323987 elements. Creating vector time with 323987 elements. Creating vector RawDepthValue with 323987 elements. Creating vector time with 323987 elements. Creating vector RawTempValue with 323987 elements. Creating vector time with 323987 elements. Creating vector Temperature with 323987 elements. Creating vector time with 323987 elements. Creating vector ErrorValue with 323987 elements. Creating vector time with 323987 elements. Creating vector bb470 with 323987 elements. Creating vector time with 323987 elements. Creating vector bb676 with 323987 elements. Creating vector time with 323987 elements. Creating vector fl676u with 323987 elements. Creating vector time with 323987 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/ctdDriver.nc') Creating vector time with 324001 elements. Creating vector conductivity with 324001 elements. Creating vector time with 324001 elements. Creating vector temperature with 324001 elements. Creating vector time with 324001 elements. Creating vector cond_frequency with 324001 elements. Creating vector time with 324001 elements. Creating vector temp_frequency with 324001 elements. Creating vector time with 324001 elements. Creating vector spare with 324001 elements. Creating vector time with 324001 elements. Creating vector humidity with 324001 elements. Creating vector time with 324001 elements. Creating vector flow1 with 324001 elements. Creating vector time with 324001 elements. Creating vector CDOM with 324001 elements. Creating vector time with 324001 elements. Creating vector dissolvedO2 with 324001 elements. Creating vector time with 324001 elements. Creating vector salinity with 324001 elements. Creating vector time with 324001 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/ctdDriver2.nc') Creating vector time with 324065 elements. Creating vector conductivity with 324065 elements. Creating vector time with 324065 elements. Creating vector temperature with 324065 elements. Creating vector time with 324065 elements. Creating vector cond_frequency with 324065 elements. Creating vector time with 324065 elements. Creating vector temp_frequency with 324065 elements. Creating vector time with 324065 elements. Creating vector flow2 with 324065 elements. Creating vector time with 324065 elements. Creating vector spare with 324065 elements. Creating vector time with 324065 elements. Creating vector salinity with 324065 elements. Creating vector time with 324065 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/isuslog.nc') Creating vector time with 62774 elements. Creating vector isusNitrate with 62774 elements. Creating vector time with 62774 elements. Creating vector isusTemp with 62774 elements. Creating vector time with 62774 elements. Creating vector isusQuality with 62774 elements. Creating vector time with 62774 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/biolume.nc') Creating vector time with 79678 elements. Creating vector rrr with 79678 elements. Creating vector time with 79678 elements. Creating vector cal_striing with 79678 elements. Creating vector time with 79678 elements. Creating vector avg_biolume with 79678 elements. Creating vector time with 79678 elements. Creating vector pump with 79678 elements. Creating vector time with 79678 elements. Creating vector system_voltage with 79678 elements. Creating vector time with 79678 elements. Creating vector flow with 79678 elements. Creating vector time with 79678 elements. Creating vector HV with 79678 elements. Creating vector time with 79678 elements. Creating vector reserved with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_0 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_1 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_2 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_3 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_4 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_5 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_6 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_7 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_8 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_9 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_10 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_11 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_12 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_13 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_14 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_15 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_16 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_17 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_18 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_19 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_20 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_21 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_22 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_23 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_24 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_25 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_26 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_27 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_28 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_29 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_30 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_31 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_32 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_33 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_34 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_35 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_36 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_37 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_38 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_39 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_40 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_41 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_42 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_43 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_44 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_45 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_46 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_47 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_48 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_49 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_50 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_51 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_52 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_53 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_54 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_55 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_56 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_57 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_58 with 79678 elements. Creating vector time with 79678 elements. Creating vector raw_59 with 79678 elements. Creating vector time with 79678 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/biolume.nc'); Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (7530 x 994) with 7484820 elements. Creating vector time with 7530 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (7530 x 994) with 7484820 elements. Creating vector time with 7530 elements. Creating vector bin with 994 elements. Creating matrix countList (7530 x 994) with 7484820 elements. Creating vector time with 7530 elements. Creating vector bin with 994 elements. Creating vector LCcount with 7530 elements. Creating vector time with 7530 elements. Creating vector transCount with 7530 elements. Creating vector time with 7530 elements. Creating vector nonTransCount with 7530 elements. Creating vector time with 7530 elements. Creating vector ai_mean with 7530 elements. Creating vector time with 7530 elements. Creating vector ai_min with 7530 elements. Creating vector time with 7530 elements. Creating vector ai_max with 7530 elements. Creating vector time with 7530 elements. Creating vector ai_std with 7530 elements. Creating vector time with 7530 elements. Creating vector esd_mean with 7530 elements. Creating vector time with 7530 elements. Creating vector esd_min with 7530 elements. Creating vector time with 7530 elements. Creating vector esd_max with 7530 elements. Creating vector time with 7530 elements. Creating vector esd_std with 7530 elements. Creating vector time with 7530 elements. Creating vector countSum with 7530 elements. Creating vector time with 7530 elements. Creating vector snapshot with 7530 elements. Creating vector time with 7530 elements. Creating vector threshold with 7530 elements. Creating vector time with 7530 elements. Creating vector sampleCount with 7530 elements. Creating vector time with 7530 elements. Creating vector flowCount with 7530 elements. Creating vector time with 7530 elements. Creating vector flowTime with 7530 elements. Creating vector time with 7530 elements. Creating vector bufferStatus with 7530 elements. Creating vector time with 7530 elements. Creating vector laserLevel with 7530 elements. Creating vector time with 7530 elements. Creating vector counter with 7530 elements. Creating vector time with 7530 elements. Creating vector counterPeriod with 7530 elements. Creating vector time with 7530 elements. Creating vector laserControl with 7530 elements. Creating vector time with 7530 elements. Creating vector countUnknownFrameCharacter with 7530 elements. Creating vector time with 7530 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7530 elements. Creating vector time with 7530 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7530 elements. Creating vector time with 7530 elements. Creating vector flowSpeed with 7530 elements. Creating vector time with 7530 elements. Creating vector countShortLFrameError with 7530 elements. Creating vector time with 7530 elements. Creating vector countGarbledLFrame with 7530 elements. Creating vector time with 7530 elements. Creating vector cFrameEsecs with 7530 elements. Creating vector time with 7530 elements. Creating vector correctedSampleCountList with 7530 elements. Creating vector time with 7530 elements. Creating vector time with 7530 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.121.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Calling build_auv_survey.m to construct survey file... SecondaryDissolvedO2 = [] Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.121.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 27 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00.mat ************************************************************************* Calling plot_sections from ../viz to produce section plots ... Using median boxcar filter of vector... Using mean boxcar filter of vector... Number of profiles found = 410 Gridding with nix = 1230, iZ = 201 Using mean boxcar filter of vector... Using mean boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Gridding... T S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp420 bbp700 fl700_uncorr N BL BLflow LOPC count transCount nonTransCount LCcount Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB420 cvarname = gB700 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount cvarname = gLOPCtransCount cvarname = gLOPCnonTransCount cvarname = gLOPCLCcount Encountered 0 NaN values in array of lon that is 393674 elements long ! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath grdtrack: Warning: -b option with type s, S, or D are deprecated; Use f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Sampled 393674 points from grid Monterey25.grd (2876 x 2447) Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 118925 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 05/01/2017 09:30 to 05/02/2017 10:29 swr = 598.9844 678.2261 870.7135 989.1695 970.6768 900.7558 741.6832 569.7391 360.7425 185.2588 37.7078 3.4221 3.0088 2.9333 2.9311 2.6822 2.6333 2.8200 2.5644 2.5776 2.8136 47.2803 229.7308 299.3004 486.0477 806.2180 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2017121_GulperTimes.txt && touch ../results/2017121_GulperTimes.txt Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017121/2017.121.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2017/2017121/2017.121.00/syslog -startEsecs 1493664014.532 -surveyName Dorado389_2017_121_00_121_00 >> ../results/2017121_GulperTimes.txt Executing: removeGulpDups.py ../results/2017121_GulperTimes.txt Bottle: 0 Time: 1493672275.66 Depth: 2.507 Dist: 9.2653 Bottle: 1 Time: 1493676997.66 Depth: 3.7632 Dist: 14.5057 Bottle: 2 Time: 1493679217.66 Depth: 2.6627 Dist: 17.0034 Bottle: 3 Time: 1493684224.06 Depth: 2.5648 Dist: 22.1944 Bottle: 4 Time: 1493686341.46 Depth: 3.0803 Dist: 23.9945 Bottle: 5 Time: 1493693998.06 Depth: 19.728 Dist: 30.375 Bottle: 6 Time: 1493703037.7287 Depth: -0.072151 Dist: 38.605 Bottle: 7 Time: 1493703122.9329 Depth: 20.0078 Dist: 38.7044 Bottle: 8 Time: 1493703192.7281 Depth: 40.0023 Dist: 38.782 Bottle: 9 Time: 1493703269.9328 Depth: 60.0209 Dist: 38.8647 Bottle: 10 Time: 1493706134.86 Depth: 10.7713 Dist: 41.4834 Bottle: 11 Time: 1493708323.66 Depth: 3.389 Dist: 43.4647 Bottle: 12 Time: 1493710812.46 Depth: 2.1665 Dist: 45.952 Bottle: 13 Time: 1493724079.86 Depth: 3.207 Dist: 58.4417 Bottle: 14 Time: 1493726383.86 Depth: 3.4957 Dist: 60.3285 Bottle: 15 Time: 1493729485.86 Depth: 5.0376 Dist: 63.1409 Bottle: 16 Time: 1493740885.726 Depth: -0.1092 Dist: 73.591 Bottle: 17 Time: 1493740986.3291 Depth: 20.0729 Dist: 73.689 Bottle: 18 Time: 1493741058.5241 Depth: 40.078 Dist: 73.7689 Bottle: 19 Time: 1493741136.9288 Depth: 60.0583 Dist: 73.8501 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_gridded.mat outvarstr = 'gF gT gN gS gD gO gB420 gB700 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth ' 2Column contouring gridded variable gD Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gO Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_2column.png Elapsed time to save image: 19 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN Drawing bottom contour from EM300 data Biolume contouring gridded variable gO Drawing bottom contour from EM300 data Biolume contouring gridded variable gB420 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB700 Drawing bottom contour from EM300 data Biolume contouring gridded variable gF Drawing bottom contour from EM300 data Biolume contouring gridded variable gBL Drawing bottom contour from EM300 data Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_biolume.png Elapsed time to save image: 68 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_lopc.png Elapsed time to save image: 17 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_2column.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing KML files ... KML = write_kml(survey_shrt_filename_base, 'Temperature', jetplus, varlimits(1,:), ctd1.T, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2017_121_00_121_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00.kml... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_121_00_121_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 414) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpBlue. Interpolating anyway. 22 NaNs found in bbpRed. Interpolating anyway. Encountered 1764 NaN values in array of lon that is 62773 elements long ! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath grdtrack: Warning: -b option with type s, S, or D are deprecated; Use f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Sampled 61009 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 61009 are not equal to number of Lat lon points = 62773 AUV track probably goes outside of the range of the .grd file being used. Setting bottom depths to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00.txt... Copied to /mbari/AUVCTD/surveys/2017/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2017/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 1 NaNs found in bbpBlue. Interpolating anyway. 22 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2017/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00.nc... Copied to /mbari/AUVCTD/surveys/2017/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2017/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_121_00_121_00.mat... Copied to /mbari/AUVCTD/surveys/2017/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2017_121_00_121_00 processed" mccann@mbari.org < mail_Dorado389_2017_121_00_121_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.121.00.mat Processing time: 832 seconds